A tree on ancestry ....
Says Isabella died after the 1888 City Directory was compiled. I might get a chance to look at the ones after 1880, but probably not today.
Here are the City Directory listings for your William Thomson and all Isabella Thompsons from 1875 to 1889. The tree owner, or whoever found the information first, says about the 1888 Directory "this is the last directory I find her in, she has moved about 2 blocks away." I don't know which of the two Isabellas he/she is referring to, the one who had lived at 121 Varick since 1879, or Isabella J who didn't appear at all in 1886.
The one living on Varick can't be your Isabella because she is listed in 1879 at a different address from your William. And a person couldn't make a case that your Isabella is Isabella J because that woman only appears in 1888, and not any of the years before that.
Bottom line: I don't think he/she has the right death information for your Isabella.
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I briefly looked for Robert and Hannah in Canada and Scotland in 1911 and didn't find them.
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** NYC City Directory
*** 1875
William Thomson, stone, h 686 Eleventh Av
Isabella Thompson, widow of Joseph h 54 W 29th [the only Isabella]
*** 1877
William Thompson, stone, h 343 E 24th
Isabella Thompson, widow of Joseph h 54 W 29th [the only Isabella]
*** 1878
image 5 says "for the year ending May 1, 1878"
William Thomson, stone, h 504 W 50th
Isabella Thompson, widow of George, h 158 W. 17th
Isabella Thompson, widow of William, h 420 East 15th
*** 1879
image 5 says "for the year ending May 1, 1879"
William Thomson, stone, h 504 W 50th
Isabella Thompson, candy, 156 W 17th
Isabella Thompson, nurse, h 121 Varick
Isabella Thompson, widow, h 420 E 15th
*** 1880
cover says "1879-1880"
image 5 says "for the year ending May 1, 1880"
William Thomson, stone, is not listed
Isabella Thompson, nurse, h 121 Varick
Isabella Thompson, widow, h 420 E 15th
Isabella Thompson, widow of George, candy, 156 W 17th
*** 1882
Isabella Thompson, widow of George, candy, 156 W 17th
Isabella Thompson, widow of John E, h 340 W 41st
Isabella Thompson, widow of William, h 420 E 15th
*** 1883
Isabella Thompson, widow of John E, h 340 W 41st
Isabella Thompson, nurse, h 121 Varick
Isabella Thompson, widow of William, h 420 E 15th
*** 1886
Isabella Thompson, widow of John E, h 420 E 15th
[the recorder must have combined the two records for the widows of John E and William]
Isabella Thompson, widow of Robert, nurse, h 121 Varick
*** 1888
Isabella Thompson, widow of Robert, nurse, h 121 Varick
Isabella J Thompson, h 402 E 117th
*** 1889
Isabella Thompson, widow of George, candy, 385 E 114th